Advanced Convert3D and ITK-SNAP Examples
This page will contain worked examples of using ITK-SNAP and C3D to perform complex tasks.
Interpolating segmentations
In this example, we create a rough segmentation of a 3D object by quickly labeling a few slices along one plane in ITK-SNAP and then using C3D to extrapolate the shape in between the drawn slices. This is useful for creating registration masks, initializing registration, etc.
Rough segmentation in ITK-SNAP
In this example we work with a postmortem hippocampus MRI scan. Labeling the whole hippocampus in this scan could take hours, and we just want a rough segmentation. So we go into ITK-SNAP and use the polygon tool to label a dozen or so slices. They do not have to be at regular intervals, as seen below.
Attach:sliceseg.png Δ
Interpolation in C3D
We perform interpolation in two stages. First, we use a distance transform with some smoothing to generate a rough 3D interpolation (which might be already good enough for some applications).
